ソフトウェア 名称 バージョン 分類 ADSCQuantumデータ収集 PHASER位相決定 REFMAC5.5.0109精密化 XDSデータ削減 XSCALEデータスケーリング
精密化 構造決定の手法 : 分子置換開始モデル : 1B4K解像度 : 2.5→49.93 Å / Cor.coef. Fo :Fc : 0.942 / Cor.coef. Fo :Fc free : 0.905 / SU B : 17.723 / SU ML : 0.181 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.276 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN ADDED IN THERfactor 反射数 %反射 Selection details Rfree 0.232 5439 5 % RANDOM Rwork 0.177 - - - all 0.18 110745 - - obs 0.18 108861 - -
溶媒の処理 イオンプローブ半径 : 0.8 Å / 減衰半径 : 0.8 Å / VDWプローブ半径 : 1.4 Å / 溶媒モデル : MASK原子変位パラメータ Biso mean : 23.16 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.7 Å2 0 Å2 0 Å2 2- - -1.25 Å2 0 Å2 3- - - -0.45 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.5→49.93 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 21476 0 228 586 22290
拘束条件 大きな表を表示 (5 x 33) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.014 0.022 22086 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 15087 X-RAY DIFFRACTION r_angle_refined_deg1.497 1.993 29857 X-RAY DIFFRACTION r_angle_other_deg0.928 3 36850 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.107 5 2810 X-RAY DIFFRACTION r_dihedral_angle_2_deg39.506 24.17 916 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.417 15 3755 X-RAY DIFFRACTION r_dihedral_angle_4_deg20.266 15 143 X-RAY DIFFRACTION r_chiral_restr0.08 0.2 3280 X-RAY DIFFRACTION r_gen_planes_refined0.007 0.021 24670 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 4229 X-RAY DIFFRACTION r_nbd_refinedX-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refinedX-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refinedX-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refinedX-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refinedX-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.503 1.5 14075 X-RAY DIFFRACTION r_mcbond_other0.123 1.5 5633 X-RAY DIFFRACTION r_mcangle_it0.974 2 22496 X-RAY DIFFRACTION r_scbond_it1.678 3 8011 X-RAY DIFFRACTION r_scangle_it2.816 4.5 7360 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Dom-ID : 1 / Ens-ID : 1 / 数 : 4385 / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (4 x 16) 大きな表を隠す Auth asym-ID タイプ Rms dev position (Å)Weight position Amedium positional0.28 0.5 Bmedium positional0.27 0.5 Cmedium positional0.28 0.5 Dmedium positional0.22 0.5 Emedium positional0.21 0.5 Fmedium positional0.23 0.5 Gmedium positional0.25 0.5 Hmedium positional0.26 0.5 Amedium thermal0.57 2 Bmedium thermal0.48 2 Cmedium thermal0.55 2 Dmedium thermal0.48 2 Emedium thermal0.45 2 Fmedium thermal0.44 2 Gmedium thermal0.45 2 Hmedium thermal0.44 2
LS精密化 シェル 解像度 : 2.5→2.56 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.318 361 - Rwork 0.273 6927 - obs - - 90.08 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 16) 大きな表を隠す ID L11 (°2 )L12 (°2 )L13 (°2 )L22 (°2 )L23 (°2 )L33 (°2 )S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2 )T12 (Å2 )T13 (Å2 )T22 (Å2 )T23 (Å2 )T33 (Å2 )Origin x (Å)Origin y (Å)Origin z (Å)1 0.6787 -0.173 -0.1495 0.5037 0.0824 0.6176 0.033 -0.0494 0.0546 -0.0113 -0.0056 -0.0714 -0.0927 0.0106 -0.0274 0.0623 -0.0178 0.0132 0.0101 0.0046 0.1002 -35.493 -29.093 36.125 2 0.2031 0.1597 -0.2079 0.3813 0.085 0.4972 0.0295 0.0034 0.0125 -0.0151 -0.0059 0.0109 -0.0414 -0.0412 -0.0237 0.107 0.0075 0.0264 0.0425 0.008 0.0889 -42.385 -32.31 33.08 3 0.4966 0.0176 0.2479 0.3926 -0.0225 0.4896 0.0402 0.0306 0.0332 -0.1289 -0.0188 0.1454 -0.0414 -0.1696 -0.0213 0.1472 0.0244 -0.0121 0.1089 0.0134 0.0961 -62.912 -42.276 20.861 4 0.4393 -0.0237 0.0511 0.9425 0.1835 0.9272 0.03 0.0525 -0.0153 -0.0798 -0.0577 0.0754 -0.0572 -0.073 0.0277 0.1165 0.0035 0.0173 0.0534 0.0099 0.0906 -56.214 -39.789 24.703 5 1.429 0.0524 0.0183 0.4927 -0.0454 0.4274 0.031 -0.0313 0.0827 0.0845 -0.0116 0.1016 -0.1105 -0.0562 -0.0194 0.1236 0.0175 0.032 0.0304 -0.0146 0.0656 -67.736 -27.053 60.231 6 0.8854 -0.0693 -0.148 0.8149 -0.295 0.5584 0.0066 -0.0152 0.0211 0.1603 0.0436 -0.0107 -0.117 -0.0154 -0.0502 0.1607 0.0027 0.0344 0.038 -0.007 0.071 -61.218 -30.056 63.978 7 1.0688 0.0852 0.2436 0.4412 -0.0581 0.5106 0.055 -0.16 0.0277 0.2294 -0.0565 -0.1095 -0.1153 0.1281 0.0015 0.2049 -0.0393 -0.0333 0.0924 -0.0021 0.0881 -40.835 -39.033 76.989 8 0.3187 0.1555 -0.1294 0.5653 -0.301 0.669 0.028 -0.0292 0.0364 0.1841 -0.024 -0.0825 -0.1275 0.0924 -0.0039 0.1983 -0.0199 -0.0041 0.0745 -0.0109 0.0838 -47.547 -36.806 73.095 9 1.1221 0.0253 0.1085 0.6493 -0.1443 0.4252 -0.0034 0.0778 -0.0694 -0.1255 -0.0201 -0.16 0.173 0.0886 0.0234 0.1716 0.0269 0.0551 0.0244 -0.0166 0.1256 -34.23 -70.265 26.198 10 0.6656 0.0027 -0.0794 1.0143 -0.3867 0.4675 0.006 0.014 -0.0388 -0.1424 -0.0509 -0.0758 0.1219 -0.0016 0.045 0.1739 0.021 0.0297 0.0328 -0.0106 0.098 -41.926 -72.503 28.574 11 0.7318 0.0564 0.0627 0.6474 -0.1207 0.6987 -0.0266 0.0485 -0.1032 -0.1145 0.0317 0.1388 0.2607 -0.12 -0.0051 0.1992 -0.0628 -0.0032 0.0474 -0.0184 0.1196 -65.012 -81.799 35.907 12 0.254 0.3259 -0.1188 0.5338 -0.1528 0.8019 -0.0238 0.0419 -0.032 -0.0838 0.0307 0.0354 0.2066 -0.029 -0.0069 0.1943 -0.0182 -0.0108 0.0441 -0.022 0.1147 -57.399 -79.06 34.012 13 1.16 0.0265 0.1179 0.7166 -0.0176 0.7612 -0.0027 -0.0936 -0.0096 0.1592 -0.0446 -0.1579 0.1235 0.1498 0.0472 0.1846 0.0421 -0.009 0.0532 0.0328 0.1045 -39.409 -80.063 67.26 14 0.5534 0.0989 0.0135 0.9397 0.4761 0.288 -0.021 -0.0686 0.0069 0.1407 0.0203 -0.0791 0.0792 0.0636 0.0007 0.2033 0.0178 -0.0025 0.0658 0.0285 0.1056 -46.926 -76.978 68.442 15 1.1607 0.0775 0.0287 0.9039 -0.0427 0.5323 -0.0003 -0.0837 -0.0616 0.1843 0.0295 0.2039 0.0796 -0.0857 -0.0292 0.1859 -0.0095 0.0722 0.0406 0.0375 0.1185 -69.993 -66.758 75.25 16 0.3651 0.1216 -0.1106 1.4702 0.1535 0.6002 -0.0415 0.0007 -0.0367 0.1906 -0.0196 0.1324 0.1081 0.02 0.0611 0.1792 -0.0095 0.0416 0.0558 0.0091 0.1026 -62.391 -69.372 73.185
精密化 TLSグループ 大きな表を表示 (5 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A1 - 213 2 X-RAY DIFFRACTION 2 A214 - 356 3 X-RAY DIFFRACTION 3 B1 - 213 4 X-RAY DIFFRACTION 4 B214 - 356 5 X-RAY DIFFRACTION 5 C1 - 213 6 X-RAY DIFFRACTION 6 C214 - 356 7 X-RAY DIFFRACTION 7 D1 - 213 8 X-RAY DIFFRACTION 8 D214 - 356 9 X-RAY DIFFRACTION 9 E1 - 213 10 X-RAY DIFFRACTION 10 E214 - 356 11 X-RAY DIFFRACTION 11 F1 - 213 12 X-RAY DIFFRACTION 12 F214 - 356 13 X-RAY DIFFRACTION 13 G1 - 213 14 X-RAY DIFFRACTION 14 G214 - 356 15 X-RAY DIFFRACTION 15 H1 - 213 16 X-RAY DIFFRACTION 16 H214 - 356